In this study, a three-dimensional hydrodynamic focusing microfluidic method is presented that allows full control of the nano-precipitation process of adamantyl mesityl BODIPY (4,4-difluoro-3,5-di-(adamantyl)-8-mesityl-4-bora-3a,4a-diaza-s-indacene) (Adambodipy). The precipitation is achieved by combining a central Adambodipy organic flow with a mixture of water and a cationic surfactant, creating a non-solvent precipitation method. The flow and mixing were simulated using COMSOL Multiphysics® 3.4. A good agreement between theory and experiment was obtained for the flow velocity, concentration fields and the subsequent precipitation kinetics. Fluorescence lifetime imaging was used to visualize the precipitation domains following the changes in fluorescence lifetime. The lifetime decreases from 6.1 ns for the molecules down to 0.9 ns for nanoparticles. A principal components analysis of the successive fluorescence decay curves showed that the process could be adequately modeled using three components, which can be attributed to monomers (single molecule), clusters (nuclei) and nanoparticles.